new msa dash

2022-09-05 16:52:45 +01:00 · 2022-09-05 16:52:45 +01:00 · e69c2a60aa
commit e69c2a60aa
parent 3037d6e3ef
4 changed files with 393 additions and 98 deletions
--- a/msa/server.R
+++ b/msa/server.R
@ -0,0 +1,105 @@
+function(input, output, session) {
+  observeEvent(
+    {
+      input$display_position_full_range #special-purpose for MSA
+      input$logoplot_colour_scheme
+      input$switch_target
+    },
+    {
+      # C O M P A T I B I L I T Y
+      #gene=input$switch_target
+      #drug=target_map[[gene]]
+      merged_df3=cbind(get(paste0(input$switch_target, '_merged_df3')))
+      
+      position_max=max(merged_df3[['position']])
+      position_min=min(merged_df3[['position']])
+      min_ligand_distance=min(merged_df3$ligand_distance)
+      max_ligand_distance=max(merged_df3$ligand_distance)
+      # FIXME: these are IMPORTANT
+      # # add "pos_count" position count column
+      # merged_df3=merged_df3 %>% dplyr::add_count(position)
+      # merged_df3$pos_count=merged_df3$n
+      # merged_df3$n=NULL
+      # 
+      mutable_df3 = cbind(merged_df3)
+      unified_msa = get(paste0(input$switch_target, '_unified_msa'))
+      # 
+      # # re-sort the dataframe according to position count
+      sorted_df = cbind(merged_df3)
+      sorted_df = sorted_df %>% arrange(pos_count)
+      
+      # 
+      outdir = paste0("~/git/Data/", drug, '/output/')
+      indir  = paste0("~/git/Data/", drug , "/input/")
+      # 
+      # source("~/git/LSHTM_analysis/scripts/plotting/logo_data_msa.R") # probably unnecessary...
+      
+      #  source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
+      
+      #### nasty special-purpose merged_df3 variants ####
+      # FIXME: SLOW
+      # corr_plotdf = corr_data_extract(
+      #   merged_df3
+      #   , gene = gene
+      #   , drug = drug
+      #   , extract_scaled_cols = F
+      # )
+      
+      #input$stability_snp_param
+      
+      updateSliderInput(
+        session, 
+        "display_position_range",
+        min = position_min,
+        max = position_max
+        #, value = c(position_min, position_min+150)
+      )
+      updateSliderInput(
+        session,
+        "display_position_full_range",
+        min = 1, 
+        max = position_max #, 
+        # value = c(position_min, position_min+150)
+      )
+      updateNumericInput(session, "selected_logop_snp_position", min = position_min, max = position_max, value = position_min)
+      updateNumericInput(session, "selected_logop_ed_position", min = position_min, max = position_max, value = position_min)
+      updateNumericInput(session, "corr_lig_dist", min = min_ligand_distance, max = max_ligand_distance, value = min_ligand_distance)
+      
+      stability_colname      = stability_boxes_df[stability_boxes_df$stability_type==input$stability_snp_param,"stability_colname"]
+      outcome_colname        = stability_boxes_df[stability_boxes_df$stability_type==input$stability_snp_param,"outcome_colname"]
+      
+      display_position_range = input$display_position_range
+      plot_min=display_position_range[1]
+      plot_max=display_position_range[2]
+      
+      display_position_full_range = input$display_position_full_range
+      full_range_min=display_position_full_range[1]
+      full_range_max=display_position_full_range[2]
+      
+      logoplot_colour_scheme = input$logoplot_colour_scheme
+      omit_snp_count = input$omit_snp_count
+      
+      print(paste0('Plotting positions between: ', plot_min, ' and ', plot_max))
+      
+      subset_mutable_df3=mutable_df3[(mutable_df3$position>=plot_min & mutable_df3$position <=plot_max),]
+      
+      subset_mutable_df3=mutable_df3[(mutable_df3$position>=plot_min & mutable_df3$position <=plot_max),]
+      subset_sorted_df=sorted_df[(sorted_df$position>=plot_min & sorted_df$position <=plot_max),]
+      
+      
+      
+      #### LogoPlotMSA/Logo Plot ED ####
+      output$LogoPlotMSA = renderPlot(
+        LogoPlotMSA(target=input$switch_target,
+                    plot_positions=full_range_min:full_range_max,
+                    my_logo_col = logoplot_colour_scheme,
+                    aa_pos_drug = aa_pos_drug,
+                    active_aa_pos = active_aa_pos,
+                    aa_pos_lig1 = aa_pos_lig1,
+                    aa_pos_lig2 = aa_pos_lig2,
+                    aa_pos_lig3 = aa_pos_lig3
+        )
+      )
+    }
+  )
+}